uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis
Class CDnaOverlapAnalysis

java.lang.Object
  extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
      extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
          extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureOverlapAnalysis
              extended by uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.CDnaOverlapAnalysis
All Implemented Interfaces:
BasicFeatureAnalysisAble

public class CDnaOverlapAnalysis
extends FeatureOverlapAnalysis

Analysis class which calculates the high scoring path in a clustered sequence using the cDNA overlap on the exon level

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
CDnaOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions, java.util.ArrayList _arrListOfCDnaRegions, SimpleArg _allArguments)
          constructor for CDnaOverlapAnalysis objects
 
Method Summary
 java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
          method which returns the high scoring path of genemodels on a sequence using the cDNA overlap on the exon level
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.FeatureAnalysis
getArrListOfFeatRegions
 
Methods inherited from class uk.ac.sanger.psu.gfmerge.analysis.simfeature_analysis.BasicFeatureAnalysis
getAllArguments, getArrListOfGMRegions, getClassName
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

CDnaOverlapAnalysis

public CDnaOverlapAnalysis(java.util.ArrayList _arrListOfGMRegions,
                           java.util.ArrayList _arrListOfCDnaRegions,
                           SimpleArg _allArguments)
constructor for CDnaOverlapAnalysis objects

Parameters:
_arrListOfGMRegions - ArrayList of genemodel regions
_arrListOfCDnaRegions - ArrayList of cDNA regions
_allArguments - SimpleArg object which contains all command line arguments
Method Detail

getHighScoringGmRegArr

public java.util.ArrayList getHighScoringGmRegArr(java.util.ArrayList _arrListOfGMRegionsToAnalyze)
method which returns the high scoring path of genemodels on a sequence using the cDNA overlap on the exon level

The overlap score is corresponding to the overlap of cDNAs at the genemodel exon level measured For further details consult the documentation.

Specified by:
getHighScoringGmRegArr in interface BasicFeatureAnalysisAble
Specified by:
getHighScoringGmRegArr in class BasicFeatureAnalysis
Parameters:
_arrListOfGMRegionsToAnalyze - ArrayList of genemodel regions
Returns:
ArrayList of regions with high scoring genemodels